Вавиловский журнал генетики и селекции. 2017;21(4):435-442 Эволюционная генетика DOI 10.18699/VJ17.262 ОБЗОР / REVIEW

Revisiting two hypotheses on the “ syndrome” in light of genomic data

A.S. Wilkins

Institute of Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany

Domesticated mammals of many different species share a set of «Синдром одомашнивания» physical and physiological traits that are not displayed by any of their wild progenitors. This suite of traits, now termed the “domestication в свете геномных данных syndrome” (DS), has been a puzzle since discovered it. Two general explanations of its basis have been proposed, which in А.С. Уилкинс principle, could also apply to other vertebrates, such as fish and birds, whose domesticated varieties show some of its elements. The two Институт теоретической биологии Берлинского ideas are termed here, respectively, the thyroid hormone hypothesis университета им. Гумбольдта, Берлин, Германия or the THH, and the cell hypothesis, the NCCH. The two ideas make distinctly different genetic predictions. Here, the current relevant evidence from genomics is evaluated and it is concluded that Доместицированные млекопитающие разных видов the NCCH has more support. Nevertheless, one set of observations, имеют общий набор физических и физиологических from chickens, suggest a potentially important role of altered thyroid признаков, которых не было у их диких предков. metabolism in domestication. In addition, recent studies indicate the Совокупность этих признаков, называемая «синдро­ possibility of additional genetic factors in domestication, affecting мом одомашнивания», остается загадкой со времен tameness and sociality, that may go beyond either hypothesis. The Чарльза Дарвина, открывшего этот феномен. В на­ tasks that lie ahead to fully ascertain the genetic bases of the “domes­ стоящее время существуют две общие гипотезы, tication syndrome” and the behaviors that characterize mammalian объясняющие это явление, которые отчасти при­ domestication are discussed briefly. менимы и к другим позвоночным, например рыбам и птицам. Одну из этих гипотез мы называем гипоте­ Key words: domestication; “”; Charles зой тиреоидных гормонов (THH), а другую – гипо­ Darwin; comparative genomics; ; neural crest cells; thyroid тезой клеток нервного гребня (NCCH). Каждая из metabolism. гипотез приводит к совершенно разным выводам на уровне генетики. Основываясь на анализе по­ следних данных геномных исследований, имеющих отношение к обсуждаемому вопросу, мы пришли к выводу, что более обоснованной выглядит гипотеза NCCH. Тем не менее ряд наблюдений, сделанных на курах, указывает на потенциально важную роль из­ мененного метаболизма тиреоидных гормонов для процесса одомашнивания. Кроме того, недав­ние исследования указывают на возможность существо­ вания дополнительных факторов ­одомашнивания, оказывающих влияние на приручаемость и социаль-­ ность и не учитываемых ни одной из рассматрива­ емых гипотез. Кратко обсуждаются задачи, направ­ ленные на выявление генетических основ «синдро­ ма одомашнивания» и особенностей поведения, специфичных для процесса одомашнивания млеко­ питающих. Ключевые слова: одомашнивание животных; «син­ дром одомашнивания»; Чарльз Дарвин; сравни­ тельная геномика; неотения; клетки нервного КАК ЦИТИРОВАТЬ ЭТУ СТАТЬЮ: гребня; метаболизм тиреоидных гормонов. Уилкинс А.С. «Синдром одомашнивания» в свете геномных данных. Вавиловский журнал генетики и селекции. 2017;21(4):435-442. DOI 10.18699/VJ17.262

HOW TO CITE THIS ARTICLE: Wilkins A.S. Revisiting two hypotheses on the “domestication syndrome” in light of genomic data. Vavilovskii Zhurnal Genetiki i Selektsii = Vavilov Jour­ nal of Genetics and Breeding. 2017;21(4):435-442. DOI 10.18699/VJ17.262

УДК 591.612:577.175.44 Поступила в редакцию 09.03.2017 г. Принята к публикации 10.05.2017 г. © АВТОР, 2017

e-mail: [email protected] he domestication of and, in particular, that of it): Charles Darwin. He had been trying to develop a theory various mammalian species, was crucial for the develop- of the of heredity since at least the early 1850s and in Tment of human civilizations (Diamond, 1999; Larson et 1868 published his monumental work on heredity, Variation al., 2014; Francis, 2015). Involving more than 20 mammalian of Animals and Plants under Domestication (Darwin, 1868). species, and a few bird and fish species, animal domestica- Darwin was writing decades before there was an experimental tion commenced in different places on different continents science of genetics, or even any kind of theoretical framework at different times but took place primarily during the past for understanding biological inheritance, and he had to rely 11–10,000 years, following the rise of (see Larson on the work of animal and plant breeders for the data he col- et al., 2014, Fig. 1). (The is one species, however, whose lected. In the course of compiling all the information for his initial domestication took place considerably earlier, and per- monumental work on heredity, he noticed that domesticated haps twice, independently, probably more than 15,000 years breeds, regardless of species, tended to share a common set of ago (Frantz et al., 2016).) visible traits, most of those listed above. (The physiological Given the historical importance of the domestication of traits of the DS were discovered much later, however.) mammals, it is of great interest to understand both its historical There are two particularly puzzling aspects of the condition. roots and its biological basis. Although there are many specific First is the variety of the different traits of the DS, which share questions about the histories of the different domestication little immediate obvious connection with each other. Second is events, the places and approximate dates for many species are the fact that the initial selection in each instance of domestica- increasingly well known (Larson et al., 2014; Francis, 2015). tion was almost certainly for tameness, permitting humans to The biology underlying domestication, however, presents a get close to the animals involved. (This pertains even to the major puzzle. Although the domestication of each species must of from , where there may not have been have involved direct or indirect selection for docility (lack deliberate taming by humans but a self-selection of individual of fear) and tameness (ability to be handled by humans), the animals who neither attacked nor fled from people around domesticated breeds of the different mammalian species all human settlements.) The other traits were apparently dragged share a distinctive suite of physical and physiological traits, along as consequences of the initial selection, through poorly not seen in their wild progenitors. The suite of traits is neither understood connections. This phenomenon, in which selection universal amongst species nor amongst all breeds of a given for one trait brings in train one or more additional, unexpected species (Sanchez-Villagra et al., 2016). Nevertheless, it is traits, Darwin termed “unconscious selection” though perhaps sufficiently generic to be seen as a signature feature of mam- “unintended co-selection” might be more apt. malian domestication. The relationship of these traits to the Darwin’s own explanation of the phenomenon was neither initial selected traits of docility and tameness, however, is not totally self-consistent nor complete. He wanted to ascribe these readily apparent. The particular secondary morphological and changes to the gentler “conditions of living” provided by the physiological traits that mark the domesticated state include: anthropogenic environment but he also realized that in many floppy ears, smaller jaws, smaller teeth, pigmentation changes cases, the characteristics were or had become heredity, hence in the coats (toward white and brown spots), reductions in not solely a function of the anthropogenic environment. Fur- adrenocortical hormone titers, increased frequency of estrus thermore, he could not explain why the particular traits seen, cycles, reduction in brain size, and alterations in concentration and not others, were the ones that appeared in association with of several brain neurotransmitters. (For a comprehensive tally the domesticated state. It is, of course, not puzzling that he of which domestication-specific traits appear in the different himself could not answer the question in the 19th century, even mammalian species that have been domesticated, see Figure 1 approximately, given the general ignorance of Mendel’s work, of Sanchez-Villagra et al., 2016.) which would eventually provide the foundations of modern This condition has been dubbed the “domestication syn- genetics. What is perhaps more surprising in retrospect is that drome”, abbreviated here as the DS. The term itself appears 20th century genetics also failed to solve the problem. Some to have been first used in connection with a parallel set of heroic and important large efforts were made, however, and observed commonalities amongst domesticated plants (Ham- a significant start was made with the work of the pioneering mer, 1984) but was later applied to animals (Larson et al., Soviet geneticist Dmitry Belyaev and his colleagues from the 2014; Wilkins et al., 2014). (Some authors, however, prefer early 1960s onwards (Belyaev, 1974, 1979; reviewed in Trut the term “domesticated ” to avoid the implication et al., 2009), but the answer remained stubbornly elusive. of illness associated with the word “syndrome”, e. g. (Leach, Today, in principle, comparative genomics should be able 2003).) That these traits are a product of domestication itself to provide the solution via comparisons of the of rather than a condition that developed independently and domesticated animals with those of their respective wild subsequently in each line is shown by their rapid appearance progenitors. This work so far, however, has not yet produced during the experimental domestication of foxes, rats and mink, a clear answer. There are two difficulties that impede a solu- which involved selection only for increased docility (Belyaev, tion. One is that, often, a reference “wild” progenitor strain is 1974; reviewed in Trut, 1999). This shows that the genetic not always known or still extant; there are ways around this, factors underlying tameness are linked in some way with the however (as discussed below). A second difficulty is that often physical and physiological traits of the DS. a wealth of genetic differences is found in each comparison between domesticated breeds and their putative ancestral Darwin’s discovery of the DS stock. The challenge is to isolate those that were crucial to The search for an explanation of the DS began with the man the initial domestication from all those that may have arisen who discovered the phenomenon (although he did not name subsequently during domestication. In effect, there are many

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“domestication genes”, the majority probably being those regulate thyroid hormone concentrations or sensitivity to those that accrued well after the first events and amplified by the hormones, triiodothyronine (T3) and its precursor tetraiodo- that later ensued. Some, perhaps many, of thyronine (T4). These hormones have long been known to those genetic changes might have involved genetic drift after affect postnatal and juvenile development but are now known various bottle-necks in breeding while numerous others would to be produced during embryonic and fetal development as be consequences of selection for particular breed-specific well. Since in postnatal development, their concentrations tend characters. Still others may reflect the fact that domestication to be higher in juvenile stages than later, the genetic changes may mobilize transposable elements whose movements create involved in the initial stages of domestication and the develop- more genetic changes (Glazko et al., 2014). ment of the DS would presumably have involved, under the Altogether, the problem of identifying the genes involved in assumption of neoteny in domestication, longer-lasting high the initial events of domestication is not so much the equivalent thyroid hormone levels in post-natal development. There is of finding a single needle (a putative causative “domestication some support for such correlations: bonobos, Pan paniscus, a gene”) in a haystack (the ) as finding what is probably putatively neotenous and “self-domesticated” species of chim- a set of specific needles (the initially selected domestication panzee (Hare et al., 2012) has significantly extended periods genes that trigger the DS) within one relatively small haystack of thyroid hormone production compared to the related non- (the total set of “domestication genes”) that itself is dispersed neotenous species, Pan troglodytes (Behringer et al., 2013). throughout a much larger haystack (the genome). A further Given the central role of altered thyroid metabolism in this complication is that, from what is known today, nothing de- hypothesis, the idea predicts that genetic changes in thyroid mands that the initiating domestication genes were always the hormone concentrations, or sensitivities to them, underlie same. In effect, there need not be a universal set of such genes; the DS. In principle, single gene changes or a very small the genomic findings, reviewed below, confirm this. “Do- number of genetic changes should be capable of producing mestication” thus may consist of a set of conditions, or even such. Thus, though this is not stated in Crockford (2002), be a continuum of states, underlain by a variety of different the genetic prediction of the THH is that domesticated lines genetic changes (Vigne, 2011; Sanchez-Villagro­ et al., 2016). should show one or a small number of changes in genes involved in thyroid hormone metabolism, which are not seen Two hypotheses in the presumed progenitor wild strains. (Conceivably, the To aid the process of identifying the relevant initial domes- could affect the development of the thyroid gland tication genetic changes, however, it would help to have a but that seems less likely since such mutations would be hypothesis about the DS. In principle, that organizing idea more likely to have strongly deleterious effects.) The THH, could help focus the search. The hypothesis should be one of course, does not exclude the possibility that domesticated that links genes and development since all the traits of the animals will have many other, additional genetic differences DS are initiated by events taking place during embryonic and from their wild forebears but posits that the number of genes fetal development. Indeed, two such ideas have been offered. needed to initiate domestication is small, even in the limiting The first focuses on thyroid hormones and the possibility case, single gene mutations. of timing shifts in development (so called “heterochronic” The other hypothesis, the neural crest cell hypothesis or changes) due to altered concentrations of these hormones in NCCH takes a different starting point: the fact that most of early development. Though not named by its proposer, I will the affected features in the DS are linked through a shared call it the “thyroid hormone hypothesis” or THH. The second cell type in their development, namely the neural crest cells posits a crucial role of alterations in neural crest cell develop- of the early embryo. Wilkins et al. (2014) proposed that all ment in the early embryo in generating the phenotypic changes the “phenes” (single phenotypic traits) of the DS might be ex- seen in the DS. It will be labeled here “the neural crest cell plained by relatively small deficits of neural crest cells in their hypothesis” or NCCH. final locations – relative to the progenitor wild breeds – after The THH was proposed by Susan Crockford (Crockford, these cells have migrated in early 2002). Its basic premise is that the DS is a reflection of “neo- from the dorsal side of the neural tube. In this view, selection teny”, a genetic shift leading to an extended juvenile develop- for docility and tameness – presumably the initial step in do- mental phase before sexual maturity is achieved. Neotenous mestication – entails selection for those properties produced as features associated with domestication include floppy ears, a consequence of mild neural crest cell deficiencies in develop- smaller jaws, and certain behavioral traits signifying prolonged ment. They further suggested that docility in the early stages juvenility. Other features, however, such as the pigmentation of domestication specifically reflected smaller adrenal glands changes and more frequent estrus cycles do not readily fit this (which derive in part from neural crest cells) producing lower description. Furthermore, it has been questioned how general concentrations of adrenocorticotropic hormones, leading to even behavioral neoteny is in domestication, though it cer- delayed and/or reduced “fight-or-flight” responses (Wilkins et tainly exists in dogs (Price, 1999). If tameness itself, however, al., 2014). (Domesticated rats and foxes, in fact, have smaller is seen as a neotenous trait – and younger animals are often adrenal glands than their wild counterparts and produce lower less frightened and more readily handled than adults – then concentrations of adrenocorticotropic hormones.) This is not domestication as a whole might be seen as a form of neoteny. the only conceivable pathway toward docility and tameness Since thyroid hormones play key roles in regulating the rates but it is reasonable and consistent with the evidence. of growth and maturation in animals, the hypothesis assigns In contrast to the THH, the NCCH posits genetic com- a major role to the thyroid hormones. In this interpretation, plexity, indeed a polygenic basis for the DS. Although many domestication involved selection for genetic changes that genes are known that affect and are required for neural crest

Эволюционная генетика Вавиловский журнал генетики и селекции • 2017 • 21 • 4 437 Revisiting two hypotheses on the “domestication A.S. Wilkins syndrome” in light of genomic data

cell formation, migration or correct cellular differentiation breeds with Przewalski’s (a wild line of that is of the cells that form from them, there are no known single- not the precursor of domesticated species but may be closely gene mutations in any species in this set of genes that create related to that stock) and those from two horse fossils from the DS, although a number of single gene mutations in this the late , approximately 43,000 and 16,000 years group of genes generate some features of the DS, especially before present (BP), dates that well precede horse domestica- pigmentation changes and mild alterations in craniofacial tion (estimated at 5,500 years from the oldest agreed fossils features (Wilkins et al., 2014). While severe loss-of-function of domesticated horses) (Schubert et al., 2014). Using several mutations in these genes tend to produce lethality or neu- tests to detect which genes and genomic regions had undergone rocristopathies, mild loss-of-function mutations should, in selection in the domesticated horse genomes, the authors con- principle, be viable. In this explanation, the DS is a product centrated on 125 target genes detected by these tests, which of the additive (or perhaps synergistic) effects of partial loss- had already been implicated as contributing to physical or of-function mutations in several, perhaps many, neural crest physiological features of domesticated horses. This set of cell genes in each domesticated line of animals. Hence, the genes largely excludes the key early developmental genes prediction of the NCCH for genomic data is that the genomes that are the focus of both the THH and the NCCH. Neverthe- of domesticated animal lines will show a number of variant less, two neural crest cell genes, the KIT and MC1R genes, neural crest cell genes that are not seen in the ancestral or known to be expressed in pigment-generating tissues derived surrogate progenitor wild-strain genomes. from neural crest cell genes, were found to show evidence of When alternative hypotheses are proposed, it is often the having undergone selection. Such selection, however, could case that both capture some aspect of reality. In this particular well reflect later events in domestication, not those involved case, it is worth noting that while the study of thyroid hor- in generating the DS. mone effects has been most extensively characterized in fetal More informative comparisons, with respect to early events development, thyroid hormones are also produced, though at in horse domestication, were presented in a recent paper by low levels, in embryos and have long been suspected to have Librado et al. (2017). They sequenced and analyzed the ge- developmental effects in that stage. This has recently been con- nomes of 14 horse skeletons from three locations in northern firmed in a study showing that inhibition of thyroid hormone Asia, dating to between 4.1 and 2.3 thousand years ago. receptor action, either by drug inhibition or knock-down of Using a new analytical method, LSD (Levels of exclusively expression, strongly reduces neural crest cell migration (Bron- Shared Differences), they detected evidence of selection for chain et al., 2016). Thus, it might be possible to link the two a variety of genes early in horse domestication. In particular, hypotheses by postulating that the “domestication syndrome” the analysis picked out a number of genes involved in neural reflects minor neural crest cell deficits as a consequence of system development, probably associated with cognitive and mild decreases of thyroid hormone during embryonic develop- behavioral differences in domestication. Of special interest ment or partial loss-of-function mutations in the receptor(s). here, however, they also detected three neural crest cell genes, This suggestion, however, conflicts with the idea that the TCOF1, KITL, and FGFR1. These genes play roles in such neotenous characteristics associated with domestication are properties as neural crest cell morphology, ear shape, cranial most readily explained by increased duration and signaling mesenchyme, and de­velopment of the mid-brain nucleus, the of thyroid hormones (see above). Nevertheless, the connec- substantia nigra (the latter containing neural crest cell-derived tion between thyroid hormones and neural crest cells should dopaminergic neurons). The authors state, “Our findings thus be remembered in considering the possible developmental support the neural crest hypothesis of animal domestication”. foundations of domestication. No genes involved in thyroid metabolism were indicated as having been detected. Comparative genomic analysis: Cats. The principal cat genomic analysis to date used two evaluating the two hypotheses living wild-cat species (one from Europe, one from the Middle In principle, as noted, comparative genomic analysis should East) as reference wild species against six domestic breeds be able to test the two ideas since they make such different (from different lineages and regions) and screened all protein- genetic predictions. To do these comparisons requires an coding genes for signs of selection (specifically, a higher appropriate reference genome, namely that of the putative dn/ ds ratio in the codons of genomes of the domesticated ones) wild stock from which the domesticate strain had been bred. after identifying regions of the genome in the domesticated Nevertheless, even if such an ancestral stock is unknown or species that looked genetically differentiated from those in the presumed extinct, the situation is not hopeless if genomes wild species. The authors found 13 genes that appear to be can be recovered from preserved bones of the presumed an- strong candidates for domestication genes by genetic criteria cestral type. Below, some of the more relevant and extensive used to detect selection (Montague et al., 2014). None of these studies, grouped by species, are reviewed. In the discussion, genes apparently has any known role in thyroid hormone the term “neural crest genes” will refer to those genes active metabolism. On the other hand, one genomic region that and required in early neural crest cell development or those had high Fst, when pooled domesticated cat genomes were activated distinctively in cell lineages derived from neural compared with those of wild cats, included the TSHR gene, crest cells. In what follows, many interesting genomic facts the gene encoding the thyroid stimulating hormone receptor. will be omitted, to keep the focus on those genetic differences This finding does not prove that this gene itself was selected, that bear specifically on the two hypotheses. nor, if it was, that it was selected at an early stage in domes- Horses. The first extensive horse genomics study involved tication but this observation is consistent with the predictions the comparison of genomes from six present-day domesticated of the THH.

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More strikingly, however, five of the 13 strong candidate mammalian lines. Not least, the fact that Belyaev’s experi- genes can be considered neural crest cell genes: they are ex- mental domestication of silver foxes, rats and mink, required pressed in neural crest cells and are necessary for full neural multiple successive generations, with selection for ever-tamer crest cell function, almost certainly in cell migration. The animals and the gradual onset of phenes of the DS is a strong first two are protocadherin genes, PCDHA1 and PCDHB4, argument for the polygenic basis of domestication. implicated in both neural crest cell migration and several Dogs. Two extensive comparative dog genomic studies, brain functions involving synapse formation. Three others are looking for genetic signs associated with domestication are ARID3B, DCC, and PLEKHH1, which are also required for of note. The first, by Axelsson et al. (2013), searched the dog neural crest cell migration. The last, PLEKHH1, also interacts genome for “candidate domestication regions”, CDRs, those with MYC, a transcriptional regulator within neural crest cells. genomic segments likely to have been targets for selection. In addition, this study also identified KIT as a domestication The comparisons were of genomes derived from 12 wolves gene, specifically as the gene responsible for the “gloving” from diverse geographical regions, and 60 dogs from 14 mod- phenotype (white paws) in the Birman breed of domestic cats. ern breeds. Altogether, the authors found 36 CDRs. The em- As mentioned above, KIT has long been known as a neural phasis in analyzing these CDRs was on searching for genes crest cell gene involved with melanocyte pigmentation and has known to be involved in features modified in domestication, also been implicated as a domestication gene in both horses hence neural system development and aspects of metabolism. (as noted above) and (Rubin et al., 2012). Altogether, Nineteen CDRs were found to be enriched in genes involved these findings support the NCCH. As the authors say, “The in neural development. A further 11 genes were identified as genetic signals from this analysis fall in line with the predic- important in this respect from a search of the literature. One tions of the domestication syndrome hypothesis (50), which of these was CRYM, a T3-binding protein important in brain posits that the morphological and physiological traits modi- function (see their Table S9), a finding consistent with the fied by mammalian domestication are explained by direct and THH. No neural crest genes were specifically identified as indirect consequences of mild neural crest cell deficits during such in this study but the candidate gene approach, focusing embryonic development” (Montague et al., 2014). on genes known to be involved in neural development and Rabbits. An extensive comparative rabbit genome analy- metabolism, would have militated against finding affected sis compared the genomes of wild rabbits from 14 different genes that are primarily involved in early development. By lo­cations in France and on the Iberian peninsula with six dif- using modern dog breeds, many of the identified differences ferent domestic species (Carneiro et al., 2014). The analysis probably reflect genetic changes in the past 200–300 years, identified SNPs in all parts of the genome – not just coding the period in which these breeds were created, not the earliest regions – that were enriched in the domesticated species. This stages of dog domestication. approach allows identification of putative regulatory control A more recent investigation, however, has focused on try- regions in addition to any changes that might be found in ing to identify genes involved in those early stages of dog coding regions. Rabbit domestication has a much shorter domestication (Pendleton et al., 2017). It involved genomic history relative to cat and horse domestication, perhaps only comparisons between wolves and village dogs found from 1,400 years, hence one might expect a comparatively weak around the world. Village dogs, unlike modern dog breeds, selection signal. Despite that, a large number of differences be- are more likely to be closer genetically to the earliest stages tween the wild and domesticated animals were found. Intrigu- of dog domestication than modern breeds are. Any significant ingly, there was an approximately 30-fold greater number of differences with respect to genomes would be candi- SNPs associated with conserved non-coding elements (CNEs), dates for domestication-related changes. This study, based these being putative regulatory regions, than with coding on the genomes of 10 wolves and 43 village dogs, identified regions. Amongst the several protein-coding gene SNPs identi- 37 CDRs, containing 172 genes in total. As with the findings fied as associated with domestication, however, were found of Axelsson et al. (2013), these included various genes affect- two well-characterized neural crest cell genes, SOX2 and ing metabolism but also genes that had not been picked up PAX2. No SNPs in genes involved in thyroid metabolism were in that earlier study. Amongst the latter were many affecting reported. various developmental aspects, such as bone development, and Significantly, no sites were found to have gone to fixation within the set of developmental genes were a large number in any of the domesticated breeds, either in CNEs or in exonic of neural crest cell genes. (For the full breakdown accord- coding regions. The implication is that domestication in the ing to functional category of the genes associated with the rabbit has involved different combinations of genes operat- CDRs, see their Table 2.) The neural crest-cell related genes ing in a quasi-additive polygenic fashion. This, indeed, is the included a number involved specifically in Wnt-, BMP- and authors’ principal conclusion from their work (Carneiro et al., FGF-signalling pathways. All were found in regions associ- 2014) and is in line with perceptions from earlier work on do- ated with selective sweeps and the inference is that many were mestication in both plants and animals that suggests that there themselves selected as part of the domestication process. (The are no single gene mutations that create the domesticated state list is given in Table, here.) The paucity of coding changes (Larson et al., 2014). The further implication is that there can found in this study in the entire set of 172 genes in the CDRs be multiple genetic routes toward domestication, even within suggests further that the changes selected were regulatory, not the same species. This is also a feature of the NCCH though changes in coding sequences. Though not providing definitive that hypothesis stresses specifically the number and variety proof, the results supply strong confirmation of the NCCH. of different neural crest cell genes that might be involved, In contrast, no genetic differences involving genes of thyroid with different sets possibly involved in different domesticated metabolism were found in this study.

Эволюционная генетика Вавиловский журнал генетики и селекции • 2017 • 21 • 4 439 Revisiting two hypotheses on the “domestication A.S. Wilkins syndrome” in light of genomic data

Genomic signatures of domestication relevant to the THH and NCCH Animal type Study Genes identified supporting THH NCCH Horses Schubert et al., 2014 – KIT, MC1R Librado et al., 2017 – TCOF1, KITL, FGFR1 Cats Montague et al., 2014 TSHR PCDHA1, PCDHD4, ARID3B, DCC, PLEKHH1, KIT Rabbits Carneiro et al., 2014 – SOX2, PAX2 Dogs Axelsson et al., 2013 CRYM – Pendleton et al., 2017 FGF13, WNT9b, WNT3, ZIC3, AXIN2, AXIN11, SMO, NOL11, SNX19, PRKCA, WF1KKN1

Current status of the two hypotheses, siveness, hence greater tameness, the defining feature of the in light of the genomics data domesticated state. The collective results of these genomic studies do not solve These findings, though involving just one gene in one bird the genetic basis of the “domestication syndrome” but they species, may, of course, have relevance to the larger phenom- are informative. The genetic differences showing signatures enon of animal domestication. It will be fascinating to see if of domestication with respect to the THH and the NCCH similar but engineered mutations in the TSHR have similar are summarized in the Table. Two genetic differences in the effects in mammals. One analysis on the genetic basis of al- combined data set are consistent with the THH but if the THH tered seasonality in rabbits picked out a number of candidate was truly the general explanation of domestication, one would genes but TSHR was not one of them (Carneiro et al., 2015). predict a much stronger signal of thyroid hormone involve- Nevertheless, if subsequent tests in mammals should indicate ment to have been detected. In contrast, the genomic work a link between TSHR and domestication, then it would be of provides much supports for the NCCH, as can be seen even interest to see how this, in turn, might connect with the grow- with a glance at the Table. ing body of evidence that supports the NCCH. Can one therefore, at this point, regard the THH as hav- ing effectively been ruled out? The answer is “no”. After all, Taking stock and looking ahead the majority of studies would probably have missed single This is a good time to take stock of our understanding of ani- nucleotide changes (SNPs) that might have affected regulatory mal domestication, in general, and the DS, in particular, and changes in thyroid metabolism in domesticates. Indeed, the then to assess what now needs to be done. In thinking about the only analysis so far that has systematically looked for SNPs , it would be hard to overestimate the throughout the genome associated with domestication, that of importance of the work of Dmitry Belyaev and his colleagues. Carneiro et al. (2014) on domesticated rabbits, found that such That work has been the crucial foundation of modern think- regions had been far more frequently selected in the course ing about animal domestication and much of the subsequent of domestication than mutations in coding sequences. This is research on it. One can identify several key elements that also an inference from the Pendleton et al. (2017) analysis of have made it so. First, they established that it is possible to dog genomes, with its findings of multiple CDRs in the dog experimentally recapitulate the process of domestication and genome but few protein-coding changes. The importance of to do so in a relatively short number of generations. Second, identifying regulatory genetic differences applies of course they showed that simply selecting for tameness brings in train to the neural crest cell genes as well as those of thyroid me- other well-known features of domestication, in effect that the tabolism. Because systematically identifying which genes are DS is an intrinsic feature of the process, not an accidental by- transcriptionally controlled by distant conserved non-coding product or later-developing concomitant. Third, Belyaev and elements, CNEs, is difficult, the road ahead may be a long one. company provided the first strong evidence that many genes In effect, the comparative genomic investigation of domes- must be involved, thus that the domesticated state truly has tication and of the DS may still be at a relatively early stage. a polygenic basis. Fourth – although this aspect has not been Apart from taking into account possible oversights in the explored in this article – they presented some good arguments analyses, however, there is a finding that supports the idea of and some initial evidence (in particular that concerning the altered thyroid hormone metabolism in domestication. It has Star in foxes) that epigenetic changes may provide been shown that a mutation in the TSHR genes in chickens the initial steps in changes associated with domestication (re- can alter photoperiod response, with reduced seasonality of viewed in Trut et al., 2009). (This idea can be related, in turn, , and more frequent egg production (Karlsson to Darwin’s emphasis on the importance of the “conditions of et al., 2015, 2016). The mutation is fixed in the domestic living” in generating the domesticated state.) To the extent that breed, the White Leghorn chicken, and not found (at least in epigenetic changes is part of the process, then something like high frequency) in the ancestral strain, Red Jungle Fowl. In the “Baldwin effect” or Waddington’s “genetic assimilation” effect, this mutation establishes one important feature of the must also have subsequently kicked in, replacing epimuta- domesticated state, increased reproduction not tied to seasons. tions with true mutations, since so much of the domestication Intriguingly, it is also tightly associated with lower aggres- genotype is based on hereditable mutations (Wilkins, 2011).

440 Vavilov Journal of Genetics and Breeding • 2017 • 21 • 4 Evolutionary genetics «Синдром одомашнивания» А.С. Уилкинс 2017 в свете геномных данных 21 • 4

Settling the role of epimutations in domestication is surely A number of these genes are involved in language-use spe- one of the main challenges ahead. cifically, an aspect of sociality that is uniquely human. The This article has focused on the genetic sources of the DS possibility that these specific traits are connected to deeper itself and has examined recent genomic evidence bearing roots in animal sociality certainly merits further investigation. on two principal hypotheses, the THH and the NCCH. The In addition, several genes in dogs that are associated specifi- tentative conclusion is that the NCCH has stronger support. cally with dog-human social interactions have been implicated Nevertheless, the recent work on the TSHR mutation in domes- in humans as risk factors in neurological diseases affecting ticated chickens, which affects both reproductive cycles and social interactions (autism and schizophrenia) (Persson et behavior, keeps alive the possibility that changes in thyroid al., 2016). Ultimately, these sorts of investigations may lead metabolism have played an important part in the domestication to new insights on a matter that is receiving more and more of animals. It will be important to see if similar observations attention, the question of whether humans can be regarded as can be recapitulated experimentally in mammals. Furthermore, a “self-domesticated” species (Brüne, 2007; Francis, 2015; and most generally, it must be remembered that the compara- Theofanopolou et al., 2017). tive genomics work, despite its breadth and depth, is still at an Such matters, of course, go well beyond the phenomenon of early stage. The roles of cis-regulatory mutations, particularly, the “domestication syndrome” as it has been defined but it is in CNE sequences has only begun to be examined; most of an intriguing thought that probing the genetic roots of animal the comparative genomics work so far has concentrated domestication may help illuminate the underlying biology of on coding sequences, while both hypotheses about the DS features of human existence that we have long thought unique implicitly place a strong emphasis on regulatory mutations. to our species. Hence, much yet remains to be learned about the genetics of domestication. It is to be hoped that definitive analysis of the Acknowledgments genomes of domesticated foxes vs those of their farm-bred I thank Richard Wrangham, W. Tecumseh Fitch and Antonio non-domesticated cousins will help illuminate the matter, since Benitez-Burraco for helpful comments on an earlier draft of fox domestication was achieved rapidly and without deliberate this article. selection for anything but tameness; this should reduce the number of potentially confounding genetic changes that have Conflict of interest occurred in the long history of well-established domesticates. The author declares no conflict of interest. In addition, now that many neural crest cell genes have been provisionally connected to domestication, it will be of inter- References est to see which of these genes is associated with particular Albert F., Carlborg O., Plyushina I., Besnier F., Hedwig D., Lauten- phenes of the DS. schläger S., Lorenz D., McIntosh J., Neumann C., Richter H., Zeis- Apart from the desirability of new findings, there is also ing C., Kozhemyakina R., Shchepina O., Kratzsch J., Trut L., Te- need for integration of a growing body of observations on upser D., Thiery J., Schöneberg T., Andersson L., Pääbo S. Genetic the genetics of behavior, particularly of tameness and social architecture of tameness in a rat model of animal domestication. interactions, with the existing ideas and findings about the Genetics. 2009;182(2):541-554. DS. 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442 Vavilov Journal of Genetics and Breeding • 2017 • 21 • 4 Evolutionary genetics